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Océane Cassan
Postdoctoral researcher in statistical learning for systems biology
Education
University of Montpellier
PhD in Systems Biology
Montpellier, France
2022 - 2019
University Claude Bernard (UCBL)
MSc in Computer Science - Artificial Intelligence
Lyon, France
2019 - 2018
National Institute of Applied Sciences (INSA)
Engineering degree in Bioinformatics and Modelling
Lyon, France
2019 - 2014
Research
Postdoc - Laboratory of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM)
Statistical learning to predict and interpret biological signals at transcription initiation sites from DNA sequence.
Montpellier, France
2024 - 2023
- Prediction of R-loops formation (DNA-RNA hybrids with roles in gene regulation and genomic instability) from low complexity DNA sequence features at transcription initiation sites. Collaborators : Rosemary Kiernan (IGH) and Jérôme Moreaux (CHU).
- Prediction of transcriptional activity at enhancers and promoters in the course of neuron differentiation from low complexity DNA sequence features and TF binding motifs. Collaborators : FANTOM6 international consortium
- Team : Joint IGMM/LIRMM/IMAG Computational Regulatory Genomics. Supervisors: Laurent Bréhélin, Charles Lecellier
PhD - Institute for Plant Sciences in Montpellier (IPSIM)
Systems biology approaches to discover regulatory pathways in plants under elevated CO\(_2\).
Montpellier, France
2022 - 2019
- Statistical inference of the gene regulatory networks in Arabidopsis thaliana under elevated CO\(_2\) and nutritional limitations. Development of novel network reconstruction methods via ensembles of regression trees or penalized linear regression based on transcriptomic data and regulatory sequences information. Computational and experimental validation of network-derived hypotheses and candidate genes.
- Genome Wide Association studies to identify genetic determinants of mineral status repsonse under elevated CO\(_2\)
- Development of an interactive suite for reproducible transcriptomic analyses and the inference of regulatory networks
- Supervisors : Antoine Martin, Sophie Lèbre
- Team : SIRENE
6 months research internship - Laboratory of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM)
Supervised statistical learning to predict chromosomic interactions in the human genome, based on CAGE data and chromatin contact data.
Montpellier, France
2019
- Supervisor : Laurent Bréhélin
- Team : Joint IGMM/LIRMM/IMAG Computational Regulatory Genomics
1 month research internship - Laboratory of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM)
Sparse logistic regression to model transcription factor combinatorics for gene regulation in human
Montpellier, France
2017
- Supervisor : Laurent Bréhélin
- Team : Joint IGMM/LIRMM/IMAG Computational Regulatory Genomics
Professional Experience
4 months internship in quantitative biology - Nanolive SA
Development of software tools for the 3D detection and tracking of biological objects in label free images
Lausanne, Switzerland
2018
Teaching Experience
Instructor of R for \(3^{rd}\) year bachelor plant biology students
University of Montpellier, France
2023 - 2021
- Good practices and scientific integrity around data analysis
- Data manipulation and visualisation in R
Instructor of Rmarkdown for Master data science students
University Paul Valery of Montpellier, France
2024 - 2020
Statistical inference of regulatory networks for Master plant biology students
University of Montpellier, France
2024 - 2022
Student supervision
N/A
N/A
2021 - 2022
- Master 2 intern in biostatistics appied to gene regulation and transcriptomics
- Master 1 data science students for an annual project on Genome-Wide-Association studies
Publications
Optimizing data integration improves Gene Regulatory Network inference in Arabidopsis thaliana
Océane Cassan, Charles-Henri Lecellier, Antoine Martin, Laurent Bréhélin, Sophie Lèbre. 2024, Bioinformatics See article
N/A
2024
Natural genetic variation underlying the negative effect of elevated CO2 on ionome composition in Arabidopsis thaliana
Océane Cassan, Léa-Lou Pimparé, Timothy Mozzanino, Cécile Fizames, Sébastien Devidal, Fabrice Roux, Alexandru Milcu, Sophie Lèbre, Alain Gojon, Antoine Martin. 2024, eLife See article
N/A
2024
A gene regulatory network reveals the effects of elevated CO\(_2\) on nutrient signaling pathways and mineral composition in Arabidopsis
Océane Cassan, Léa-Lou Pimparé, Antoine Beckers, Alain Gojon, Liên Bach, Christian Dubos, Sophie Lèbre, Antoine Martin. 2023, New Phytologist. See article
N/A
2023
The decline of plant mineral nutrition under rising CO\(_2\): physiological and molecular aspects of a bad deal
Alain Gojon, Océane Cassan, Liên Bach, Laurence Lejay, Antoine Martin. 2022 Review article, Trends in Plant Science. See article
N/A
2022
Loss of Polycomb proteins CLF and LHP1 leads to excessive RNA degradation in Arabidopsis
David Séré, Océane Cassan, Fanny Bellegarde, Cécile Fizames, Jossia Boucherez, Geoffrey Schivre, Jacinthe Azevedo, Thierry Lagrange, Alain Gojon, Antoine Martin. 2022 Journal of Experimental Botany. See article
N/A
2022
Inferring and Analyzing Gene Regulatory Networks from Multi-Factorial Expression Data: A Complete and Interactive Suite
Océane Cassan, Sophie Lèbre, and Antoine Martin. 2021 BMC Genomics 22 (1). See article
N/A
2021
Probing Transcription Factor Combinatorics in Different Promoter Classes and in Enhancers
Vandel Jimmy, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, and Laurent Bréhélin. 2019 BMC Genomics 20 (1): 1–19. See article
N/A
2019
Conferences and seminars
ISMB
Speaker & poster presenter
Montreal, Canada
2024
- A machine-learning guided approach to explore the cis-regulatory code involved in neuronal differentiation. Awarded Best Postdoc Poster in the Regsys track.
FANTOM6 consortium meeting
Speaker
Milan, Italy
2023
- Probing the contribution of DNA low complexity regions in transcriptional regulations during neuron differentiation
ISMB-ECCB
Speaker
Lyon, France
2023
- Gene-specific optimisation of data integration in regression-based Gene Regulatory Network inference. Awarded the best oral presentation in the NETBIO session.
Machine Learning in Montpellier, Theory & Practice
Speaker
University of Montpellier, France
2022
- Discussing : Reconciling modern machine-learning practice and the classical bias–variance trade-off, Belkin et al, 2019.
Molecular responses of plants facing climate change
Organizer and poster presenter
Montpellier, France
2022
- Genetic determinants of the mineral status response under elevated CO\(_2\) in Arabidopsis populations
JOBIM
Poster presenter
Virtual
2021
- Dashboard for the Inference and Analysis of Networks from Expression data
International Plant Systems Biology
Poster presenter
Virtual
2021
- Gene Regulatory Network inference of Arabidopsis under elevated CO\(_2\) and nutritional limitations
Netbio, biological networks inference
Speaker
Virtual
2020
- Presenting the Dashboard for the Inference and Analysis of Networks from Expression data
Methods and Algorithms for Bioinformatics Seminars
Organizer
Montpellier, France
2024 - 2023
- Co-planner (with Eric Rivals) of regular team seminars on the topic of bioinformatics
Academic referees
PhD:
Antoine Martin, senior researcher in plant biology, head of SIRENE team, IPSiM, CNRS : antoine.martin@cnrs.fr
Sophie Lèbre, lecturer and researcher in statistics, IMAG, University of Montpellier, University Paul Valéry : sophie.lebre@umontpellier.fr
Postdoc: